Operations at the Blair Athol open-cut mine, near Clermont in central Queensland, finished in November 2012, following a 28-year production run that saw coal shipped to Japan.

But workers on individual contracts were given much more generous payouts than those on collective agreements.

The Construction Forestry Mining and Energy Union has filed a claim in the Federal Court's NSW registry, arguing the differing levels of redundancy pay discriminate against union members, and are in breach of the Fair Work Act.

The union's Sydney-based national legal director, Alex Bukarica, said the case could have wider consequences if the CFMEU has a win.

"It will test whether a company can apply its own policy in a discriminatory way," he said today.

"If we're successful ... it will have ramifications if other companies are adopting the same practices."

Rio Tinto has argued its redundancy payout system is fair.

The CFMEU says that when 70 full-time production and engineering staff were made redundant last year, non-union employees were given a redundancy payout based on their entire salary, including compulsory overtime and bonuses.

They were also given an extra three months' pay as part of their redundancy.

Conversely, unionised staff were given redundancy payments based on their base salary only.

"They have treated them less favourably because they have chosen to bargain collectively," Mr Bukarica said.

For a retrenched worker on an average $120,000 base salary, that could mean the difference between a union member walking away with $80,000 and an individual contract employee leaving with more than $150,000, he said.

Rio Tinto has defended its practice of having a two-tiered redundancy scheme, arguing union members on collective agreements had benefitted from secure working conditions.

"Employees at Blair Athol Mine were able to choose whether they worked under the collective agreement or on individual arrangements," a company spokesman said in a statement.

"Redundancy payments were made in accordance with the employee's conditions of employment, which Rio Tinto believes was fair."